Contacts of the strand formed by residues 623 - 629 (chain C) in PDB entry 1HEJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 623 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577C THR* 4.9 10.1 - - - -
578C TYR 3.1 8.5 - - - -
579C SER* 3.4 26.0 + - - -
580C VAL 4.2 0.5 + - - -
602C TRP* 5.4 0.2 - - - -
603C ASN* 2.7 34.1 + - - +
622C ASN* 1.3 81.3 - - - +
624C PHE* 1.3 57.7 - - - +
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Residues in contact with PHE 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562C VAL* 5.3 0.4 - - + -
577C THR* 5.0 2.7 - - - +
578C TYR* 3.3 57.3 + + + +
586C TRP* 3.2 42.6 - + + -
590C LEU* 4.8 19.1 - - + -
601C SER* 5.2 0.9 - - - -
602C TRP* 3.3 16.6 - - - +
603C ASN* 3.7 0.4 - - - -
604C ALA* 3.4 22.4 - - + -
606C LEU* 4.0 23.6 - - + -
615C ALA* 5.0 2.7 - - + -
623C SER* 1.3 74.6 - - - +
625C GLY* 1.3 60.3 + - - +
626C VAL* 2.9 37.9 - - + -
639C ALA* 5.1 1.1 - - + -
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Residues in contact with GLY 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575C ASN* 3.4 2.5 - - - -
576C VAL 3.7 9.4 - - - -
577C THR* 4.8 5.2 - - - -
601C SER* 3.1 23.5 - - - -
602C TRP* 3.3 40.2 + - - +
624C PHE* 1.3 71.7 - - - +
626C VAL* 1.3 70.3 + - - +
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Residues in contact with VAL 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575C ASN* 2.4 26.6 + - - +
576C VAL 3.3 4.1 + - - -
578C TYR* 4.3 4.9 - - + -
590C LEU* 6.1 2.0 - - + -
598C VAL* 3.5 32.3 - - + -
600C SER 3.5 3.6 - - - +
601C SER* 4.3 1.8 - - - -
606C LEU* 3.7 10.5 - - + -
624C PHE* 2.9 44.2 - - + -
625C GLY* 1.3 74.1 - - - +
627C THR* 1.3 59.8 + - - +
628C PHE* 3.0 50.1 - - + -
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Residues in contact with THR 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570C TRP* 4.1 14.8 - - + -
573C ARG* 4.1 24.2 - - + -
574C PHE 3.7 3.6 - - - +
575C ASN* 2.6 23.2 + - - +
598C VAL* 3.4 18.2 - - - -
599C GLN* 3.6 39.1 + - + +
600C SER* 3.1 19.5 + - - -
602C TRP* 4.4 1.7 - - - -
626C VAL* 1.3 73.9 - - - +
628C PHE* 1.3 77.0 + - - +
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Residues in contact with PHE 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573C ARG* 3.6 5.9 - - - -
574C PHE* 2.9 69.0 + + + -
576C VAL* 3.5 7.6 - - + -
578C TYR* 3.3 28.0 - + - -
590C LEU* 5.0 7.2 - - + -
592C LEU* 3.7 26.7 - - + -
596C GLN* 4.2 8.5 - - + -
597C SER 3.6 7.6 - - - -
598C VAL* 4.2 7.0 - - + -
626C VAL* 3.0 54.7 - - + -
627C THR* 1.3 77.5 - - - +
629C TYR* 1.3 63.9 + - - +
630C LYS 3.6 0.3 + - - -
637C PRO* 3.5 16.6 - - + -
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Residues in contact with TYR 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572C ASP* 5.2 2.0 - - + -
573C ARG* 3.3 41.5 + - + -
574C PHE* 4.8 0.6 - - - -
595C GLY 5.3 1.1 - - - +
596C GLN* 3.0 30.7 - - - +
597C SER* 3.4 36.5 + - - +
598C VAL 5.3 0.2 - - - -
599C GLN* 3.2 41.8 + - + +
628C PHE* 1.3 72.4 - - - +
630C LYS* 1.3 61.2 + - - +
631C ASN* 4.0 29.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il